So, I'm going to preface this by saying that this is how it works in the Challenger 300/350, which I fly.... I don't fly the 650 and have not yet looked that close at it, but I have no reason to believe Bombardier and Collins would approach this any differently between airplanes.
TAKEOFF REF page 3/4 presents several options that you can enter (see attachment). One is OBST HT and OBST DIST. LEVEL-OFF HT is also included. You enter the obstacle height and distance from "reference zero", which is the end of the takeoff distance to 35 feet (dry) or 15 feet (wet). Because they measure the obstacle's distance from reference zero, unused runway must be added to the obstacle's distance from the end of the runway. This also is a clue as to what data Collins and Bombardier are using with the calculation.
This "Obstacle Clearance Calculator" that Bombardier & Collins are using references the AFM Performance Section's Flight Path charts, both close-in and distant. These charts have been digitized and stored in the FMS's performance module. The Obstacle Clearance Calculator is using the obstacle distance from reference zero and the obstacle's height above the runway elevation to determine the required Reference Climb Gradient necessary to clear the obstacle. The reference climb gradient is equal to the 2nd segment climb gradient achieved after the landing gear has retracted, but the flaps are still in the takeoff configuration, and the thrust is at the takeoff thrust setting. The airspeed is V2 speed. Further, all of this data is based on an engine failure at VEF or the presumed engine failure speed, which is typically 1 second prior to V1 speed with the pilot electing to continue the takeoff.
The calculator will also calculate the level-off height necessary to clear the obstacle in this second segment climb, after which the aircraft can level, accelerate, and clean up to VFTO speed. That is of course assuming that this is the most critical obstacle for the takeoff. The FMS defaults to a 1000' level-off height but can extend to a higher level off height as needed. It can also be set to minimum height of 400'.
The AFM's Flight Path graphic illustrates the profile that is flown. The FMS Takeoff Ref Page 3/4 is calculating the required climb gradient flight path during the first segment climb and the second segment climb up to the calculated Gross Level-Off Height. The required Reference Climb Gradient will ensure that the Net Takeoff Flight Path clears the obstacle. The actual, or "Gross" flight path will clear the obstacle by much more, approximately 0.8% of the distance traveled from reference zero.
The Obstacle Clearance Limit weight is calculated based on the data you entered.
The system can work backwards, too. You can enter a required climb gradient in the REQ CLB GRAD field and have it calculated the limit weight. The problem is that we don't know that value. It's not the SID or ODP climb gradient since 1) those are based on all-engines operating, normal takeoff performance, and 2) the reference climb gradient data in the FMS is based on the limited scope of the two flight path charts, close-in and distant. On the distant chart, once you get beyond that vertical line on the right of the chart, you're exceeding the 5 minute time limit for takeoff thrust.
If you want to know how to comply with a SID or ODP climb gradient, I refer you to this FAA Information for Operators (InFO) bulletin: InFO 18014: Compliance with Title 14 of the Code of Federal Regulations (14 CFR) Part 97 Instrument Flight Rules (IFR) Departure Procedure & Missed Approach Climb Gradient Requirements (faa.gov)
The more I look at the CL650's FMS guide and the AFM, the more that I am fairly certain that it works the same way as in our CL300/350.
We do not use this FMS feature. Rather we along with most other operators are now using some type airport runway analysis. In the flight simulator world, these are the type of takeoff performance reports generated by the TOPCAT system: FlightSimSoft.com. Unfortunately, we're not likely to see the CL350 added to the list of airplanes supported.
I hope this helps!
Rich Boll